Showing papers by "University of Tsukuba published in 2005"

A haplotype map of the human genome

Abstract: Inherited genetic variation has a critical but as yet largely uncharacterized role in human disease. Here we report a public database of common variation in the human genome: more than one million single nucleotide polymorphisms (SNPs) for which accurate and complete genotypes have been obtained in 269 DNA samples from four populations, including ten 500-kilobase regions in which essentially all information about common DNA variation has been extracted. These data document the generality of recombination hotspots, a block-like structure of linkage disequilibrium and low haplotype diversity, leading to substantial correlations of SNPs with many of their neighbours. We show how the HapMap resource can guide the design and analysis of genetic association studies, shed light on structural variation and recombination, and identify loci that may have been subject to natural selection during human evolution.

The Transcriptional Landscape of the Mammalian Genome

Abstract: This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5' and 3' boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.

Angiotensin-converting enzyme 2 protects from severe acute lung failure

Abstract: Acute respiratory distress syndrome (ARDS), the most severe form of acute lung injury, is a devastating clinical syndrome with a high mortality rate (30-60%) (refs 1-3). Predisposing factors for ARDS are diverse and include sepsis, aspiration, pneumonias and infections with the severe acute respiratory syndrome (SARS) coronavirus. At present, there are no effective drugs for improving the clinical outcome of ARDS. Angiotensin-converting enzyme (ACE) and ACE2 are homologues with different key functions in the renin-angiotensin system. ACE cleaves angiotensin I to generate angiotensin II, whereas ACE2 inactivates angiotensin II and is a negative regulator of the system. ACE2 has also recently been identified as a potential SARS virus receptor and is expressed in lungs. Here we report that ACE2 and the angiotensin II type 2 receptor (AT2) protect mice from severe acute lung injury induced by acid aspiration or sepsis. However, other components of the renin-angiotensin system, including ACE, angiotensin II and the angiotensin II type 1a receptor (AT1a), promote disease pathogenesis, induce lung oedemas and impair lung function. We show that mice deficient for Ace show markedly improved disease, and also that recombinant ACE2 can protect mice from severe acute lung injury. Our data identify a critical function for ACE2 in acute lung injury, pointing to a possible therapy for a syndrome affecting millions of people worldwide every year.

The genome of the social amoeba Dictyostelium discoideum

Abstract: The social amoebae are exceptional in their ability to alternate between unicellular and multicellular forms. Here we describe the genome of the best-studied member of this group, Dictyostelium discoideum. The gene-dense chromosomes of this organism encode approximately 12,500 predicted proteins, a high proportion of which have long, repetitive amino acid tracts. There are many genes for polyketide synthases and ABC transporters, suggesting an extensive secondary metabolism for producing and exporting small molecules. The genome is rich in complex repeats, one class of which is clustered and may serve as centromeres. Partial copies of the extrachromosomal ribosomal DNA (rDNA) element are found at the ends of each chromosome, suggesting a novel telomere structure and the use of a common mechanism to maintain both the rDNA and chromosomal termini. A proteome-based phylogeny shows that the amoebozoa diverged from the animal-fungal lineage after the plant-animal split, but Dictyostelium seems to have retained more of the diversity of the ancestral genome than have plants, animals or fungi.

Molecular mechanisms activating the Nrf2-Keap1 pathway of antioxidant gene regulation.

Abstract: Several years have passed since NF-E2-related factor 2 (Nrf2) was demonstrated to regulate the induction of genes encoding antioxidant proteins and phase 2 detoxifying enzymes. Following a number of studies, it was realized that Nrf2 is a key factor for cytoprotection in various aspects, such as anticarcinogenicity, neuroprotection, antiinflammatory response, and so forth. These widespread functions of Nrf2 spring from the coordinated actions of various categories of target genes. The activation mechanism of Nrf2 has been studied extensively. Under normal conditions, Nrf2 localizes in the cytoplasm where it interacts with the actin binding protein, Kelch-like ECH associating protein 1 (Keap1), and is rapidly degraded by the ubiquitin-proteasome pathway. Signals from reactive oxygen species or electrophilic insults target the Nrf2-Keap1 complex, dissociating Nrf2 from Keap1. Stabilized Nrf2 then translocates to the nuclei and transactivates its target genes. Interestingly, Keap1 is now assumed to be a substrate-specific adaptor of Cul3-based E3 ubiquitin ligase. Direct participation of Keap1 in the ubiquitination and degradation of Nrf2 is plausible. The Nrf2-Keap1 system is present not only in mammals, but in fish, suggesting that its roles in cellular defense are conserved throughout evolution among vertebrates. This review article recounts recent knowledge of the Nrf2-Keap1 system, focusing especially on the molecular mechanism of Nrf2 regulation.

Measurement of atmospheric neutrino oscillation parameters by Super-Kamiokande I

Abstract: We present a combined analysis of fully-contained, partially-contained and upward-going muon atmospheric neutrino data from a 1489 d exposure of the Super-Kamiokande detector. The data samples span roughly five decades in neutrino energy, from 100 MeV to 10 TeV. A detailed Monte Carlo comparison is described and presented. The data is fit to the Monte Carlo expectation, and is found to be consistent with neutrino oscillations of {nu}{sub {mu}}{r_reversible}{nu}{sub {tau}} with sin{sup 2}2{theta}>0.92 and 1.5x10{sup -3}<{delta}m{sup 2}<3.4x10{sup -3} eV{sup 2} at 90% confidence level.

Phosphoinositide phosphatase activity coupled to an intrinsic voltage sensor

Abstract: Changes in membrane potential affect ion channels and transporters, which then alter intracellular chemical conditions. Other signalling pathways coupled to membrane potential have been suggested1,2,3 but their underlying mechanisms are unknown. Here we describe a novel protein from the ascidian Ciona intestinalis that has a transmembrane voltage-sensing domain homologous to the S1–S4 segments of voltage-gated channels and a cytoplasmic domain similar to phosphatase and tensin homologue. This protein, named C. intestinalis voltage-sensor-containing phosphatase (Ci-VSP), displays channel-like ‘gating’ currents and directly translates changes in membrane potential into the turnover of phosphoinositides. The activity of the phosphoinositide phosphatase in Ci-VSP is tuned within a physiological range of membrane potential. Immunocytochemical studies show that Ci-VSP is expressed in Ciona sperm tail membranes, indicating a possible role in sperm function or morphology. Our data demonstrate that voltage sensing can function beyond channel proteins and thus more ubiquitously than previously realized.

Disruption of Nrf2 enhances susceptibility to severe airway inflammation and asthma in mice.

Abstract: Oxidative stress has been postulated to play an important role in the pathogenesis of asthma; although a defect in antioxidant responses has been speculated to exacerbate asthma severity, this has been difficult to demonstrate with certainty. Nuclear erythroid 2 p45-related factor 2 (Nrf2) is a redox-sensitive basic leucine zipper transcription factor that is involved in the transcriptional regulation of many antioxidant genes. We show that disruption of the Nrf2 gene leads to severe allergen-driven airway inflammation and hyperresponsiveness in mice. Enhanced asthmatic response as a result of ovalbumin sensitization and challenge in Nrf2-disrupted mice was associated with more pronounced mucus cell hyperplasia and infiltration of eosinophils into the lungs than seen in wild-type littermates. Nrf2 disruption resulted in an increased expression of the T helper type 2 cytokines interleukin (IL)-4 and IL-13 in bronchoalveolar lavage fluid and in splenocytes after allergen challenge. The enhanced severity of the asthmatic response from disruption of the Nrf2 pathway was a result of a lowered antioxidant status of the lungs caused by lower basal expression, as well as marked attenuation, of the transcriptional induction of multiple antioxidant genes. Our studies suggest that the responsiveness of Nrf2-directed antioxidant pathways may act as a major determinant of susceptibility to allergen-mediated asthma.

MafA Is a Key Regulator of Glucose-Stimulated Insulin Secretion

Abstract: MafA is a transcription factor that binds to the promoter in the insulin gene and has been postulated to regulate insulin transcription in response to serum glucose levels, but there is no current in vivo evidence to support this hypothesis. To analyze the role of MafA in insulin transcription and glucose homeostasis in vivo, we generated MafA-deficient mice. Here we report that MafA mutant mice display intolerance to glucose and develop diabetes mellitus. Detailed analyses revealed that glucose-, arginine-, or KCl-stimulated insulin secretion from pancreatic beta cells is severely impaired, although insulin content per se is not significantly affected. MafA-deficient mice also display age-dependent pancreatic islet abnormalities. Further analysis revealed that insulin 1, insulin 2, Pdx1, Beta2, and Glut-2 transcripts are diminished in MafA-deficient mice. These results show that MafA is a key regulator of glucose-stimulated insulin secretion in vivo.

Lactosylated poly(ethylene glycol)-sIRNA conjugate through acid-labile β-thiopropionate linkage to construct pH-sensitive polyion complex micelles achieving enhanced gene silencing in hepatoma cells

Abstract: The remarkably enhanced gene silencing in hepatoma cells was achieved by assembling lactosylated-PEG−siRNA conjugates bearing acid-labile β-thiopropionate linkages into polyion complex (PIC) micelles through the mixing with poly(l-lysine). The PIC micelles with clustered lactose moieties on the periphery were successfully transported into hepatoma cells in a receptor-mediated manner, releasing hundreds of active siRNA molecules into the cellular interior responding to the pH decrease in the endosomal compartment. Eventually, almost 100 times enhancement in gene silencing activity compared to that of the free conjugate was achieved for the micelle system, facilitating the practical utility of siRNA therapeutics.

Acetylation of Foxo1 alters its DNA-binding ability and sensitivity to phosphorylation

Abstract: The FOXO family of forkhead transcription factors plays a key role in a variety of biological processes, including metabolism, cell proliferation, and oxidative stress response. We previously reported that Foxo1, a member of the FOXO family, is regulated through reversible acetylation catalyzed by histone acetyltransferase cAMP-response element-binding protein (CREB)-binding protein (CBP) and NAD-dependent histone deacetylase silent information regulator 2, and that the acetylation at Lys-242, Lys-245, and Lys-262 of Foxo1 attenuates its transcriptional activity. However, the molecular mechanism by which acetylation modulates Foxo1 activity remains unknown. Here, we show that the positive charge of these lysines in Foxo1 contributes to its DNA-binding, and acetylation at these residues by CBP attenuates its ability to bind cognate DNA sequence. Remarkably, we also show that acetylation of Foxo1 increases the levels of its phosphorylation at Ser-253 through the phosphatidylinositol 3-kinase–protein kinase B signaling pathway, and this effect was overridden on the acetylation-deficient Foxo1 mutant. Furthermore, in in vitro kinase reactions, the association of wild-type Foxo1 and its target DNA sequence inhibits the protein kinase B-dependent phosphorylation of Foxo1, whereas mutated Foxo1 proteins, which mimic constitutively acetylated states, are efficiently phosphorylated even in the presence of the DNA. These results suggest that acetylation regulates the function of Foxo1 through altering the affinity with the target DNA and the sensitivity for phosphorylation.

Distinct Roles of GIGANTEA in Promoting Flowering and Regulating Circadian Rhythms in Arabidopsis

Abstract: The circadian clock acts as the timekeeping mechanism in photoperiodism. In Arabidopsis thaliana, a circadian clock–controlled flowering pathway comprising the genes GIGANTEA (GI), CONSTANS (CO), and FLOWERING LOCUS T (FT) promotes flowering specifically under long days. Within this pathway, GI regulates circadian rhythms and flowering and acts earlier in the hierarchy than CO and FT, suggesting that GI might regulate flowering indirectly by affecting the control of circadian rhythms. We studied the relationship between the roles of GI in flowering and the circadian clock using late elongated hypocotyl circadian clock associated1 double mutants, which are impaired in circadian clock function, plants overexpressing GI (35S:GI), and gi mutants. These experiments demonstrated that GI acts between the circadian oscillator and CO to promote flowering by increasing CO and FT mRNA abundance. In addition, circadian rhythms in expression of genes that do not control flowering are altered in 35S:GI and gi mutant plants under continuous light and continuous darkness, and the phase of expression of these genes is changed under diurnal cycles. Therefore, GI plays a general role in controlling circadian rhythms, and this is different from its effect on the amplitude of expression of CO and FT. Functional GI:green fluorescent protein is localized to the nucleus in transgenic Arabidopsis plants, supporting the idea that GI regulates flowering in the nucleus. We propose that the effect of GI on flowering is not an indirect effect of its role in circadian clock regulation, but rather that GI also acts in the nucleus to more directly promote the expression of flowering-time genes.

Supercritical Accretion Flows around Black Holes: Two-dimensional, Radiation Pressure-dominated Disks with Photon Trapping

Abstract: The quasi-steady structure of supercritical accretion flows around a black hole is studied based on two-dimensional radiation-hydrodynamic (2D-RHD) simulations. The supercritical flow is composed of two parts: the disk region and the outflow regions above and below the disk. Within the disk region the circular motion and the patchy density structure are observed, which is caused by Kelvin-Helmholtz instability and probably by convection. The mass accretion rate decreases inward, roughly in proportion to the radius, and the remaining part of the disk material leaves the disk to form the outflow because of the strong radiation pressure force. We confirm that photon trapping plays an important role within the disk. Thus, matter can fall onto the black hole at a rate exceeding the Eddington rate. The emission is highly anisotropic and moderately collimated so that the apparent luminosity can exceed the Eddington luminosity by a factor of a few in the face-on view. The mass accretion rate onto the black hole increases with the absorption opacity (metallicity) of the accreting matter. This implies that the black hole tends to grow faster in metal-rich regions, such as in starburst galaxies or star-forming regions.

GATA1 function, a paradigm for transcription factors in hematopoiesis.

Abstract: TRANSCRIPTIONAL CONTROL OF HEMATOPOIESIS The development of mature blood cells of distinct lineages, from the hematopoietic stem cells (HSCs), involves a progressive restriction of differentiation potential and the establishment of lineage-specific gene expression profiles (Fig. 1). The establishment of these expression profiles relies on lineagespecific transcription factors to modulate the expression of their target genes. Therefore, hematopoiesis is an excellent model system to investigate how particular transcription factors influence the establishment of lineage-specific expression profiles and how their activity is regulated. In this review we focus on the present knowledge of the biological functions of the hematopoietic transcription factor GATA1. Many aspects of its function have been revealed since its first description in 1988. Yet many new questions have surfaced, and many old questions remain to be answered. Thus, GATA1 has been in the floodlight of modern biology as a paradigm for hematopoietic transcription factors in general and GATA factors in particular.

Blue Light-Emitting Diode Based on ZnO

Abstract: A near-band-edge bluish electroluminescence (EL) band centered at around 440 nm was observed from ZnO p–i–n homojunction diodes through a semi-transparent electrode deposited on the p-type ZnO top layer. The EL peak energy coincided with the photoluminescence peak energy of an equivalent p-type ZnO layer, indicating that the electron injection from the n-type layer to the p-type layer dominates the current, giving rise to the radiative recombination in the p-type layer. The imbalance in charge injection is considered to originate from the lower majority carrier concentration in the p-type layer, which is one or two orders of magnitude lower than that in the n-type one. The current-voltage characteristics showed the presence of series resistance of several hundreds ohms, corresponding to the current spread resistance within the bottom n-type ZnO. The employment of conducting ZnO substrates may solve the latter problem.

Plastid proteins crucial for symbiotic fungal and bacterial entry into plant roots

Abstract: The roots of most higher plants form arbuscular mycorrhiza, an ancient, phosphate-acquiring symbiosis with fungi, whereas only four related plant orders are able to engage in the evolutionary younger nitrogen-fixing root-nodule symbiosis with bacteria1. Plant symbioses with bacteria and fungi require a set of common signal transduction components that redirect root cell development2,3. Here we present two highly homologous genes from Lotus japonicus, CASTOR and POLLUX, that are indispensable for microbial admission into plant cells and act upstream of intracellular calcium spiking4, one of the earliest plant responses to symbiotic stimulation. Surprisingly, both twin proteins are localized in the plastids of root cells, indicating a previously unrecognized role of this ancient endosymbiont in controlling intracellular symbioses that evolved more recently.

Measurement of the J/ψ meson and b-hadron production cross sections in pp̄ collisions at √s = 1960 GeV

Abstract: The authors present a new measurement of the inclusive and differential production cross sections of J/{psi} mesons and b-hadrons in proton-antiproton collisions at {radical}s = 1960 GeV The data correspond to an integrated luminosity of 397 pb{sup -1} collected by the CDF Run II detector They find the integrated cross section for inclusive J/{psi} production for all transverse momenta from 0 to 20 GeV/c in the rapidity range |y| 125 GeV/c They find the total cross section for b-hadrons, including both hadrons and anti-hadrons, decaying to J/{psi} with transverse momenta greater than 125 GeV/c in the rapidity range |y(J/{psi})| < 06, is 0330 {+-} 0005(stat){sub -0033}{sup +0036}(syst) {mu}b Using a Monte Carlo simulation of the decay kinematics of b-hadrons to all final states containing a J/{psi}, they extract the first measurement of the total single b-hadron cross section down to zero transverse momentum at {radical}s = 1960 GeV They find the total single b-hadron cross section integrated over all transverse momenta for b-hadrons in themore » rapidity range |y| < 06 to be 176 {+-} 04(stat){sub -23}{sup +25}(syst) {mu}b« less

Three-dimensional and high-speed swept-source optical coherence tomography for in vivo investigation of human anterior eye segments

Abstract: A two- and three-dimensional swept source optical coherence tomography (SS-OCT) system, which uses a ready-to-ship scanning light source, is demonstrated. The light source has a center wavelength of 1.31 mum, -3 dB wavelength range of 110 nm, scanning rate of 20 KHz, and high linearity in frequency scanning. This paper presents a simple calibration method using a fringe analysis technique for spectral rescaling. This SS-OCT system is capable of realtime display of two-dimensional OCT and can obtain three-dimensional OCT with a measurement time of 2 s. In vivo human anterior eye segments are investigated two- and three-dimensionally. The system sensitivity is experimentally determined to be 114 dB. The three-dimensional OCT volumes reveal the structures of the anterior eye segments, which are difficult to observe in two-dimensional OCT images.

Control method of robot suit HAL working as operator's muscle using biological and dynamical information

Abstract: For assisting human motion, assistive devices working as muscles would be useful. A robot suit HAL (hybrid assistive limb) has been developed as an assistive device for lower limbs. Human can appropriately produce muscle contraction torque and control joint viscoelasticity by muscle effort such as co-contraction. Thus, to implement functions equivalent to human muscles using HAL, it is necessary to control viscoelasticity of HAL as well as to produce torque in accordance with operator's intention. Therefore the purpose of this study is to propose a control method of HAL using biological and motion information. In this method, HAL produces torque corresponding to muscle contraction torque by referring to the myoelectricity that is biological information to control operator's muscles. In addition, the viscoelasticities of HAL are adjusted in proportion to operator's viscoelasticity that is estimated from motion information by using an on-line parameter identification method. To evaluate the effectiveness of the proposed method, the method was applied to a swinging motion of a lower leg. When this method was applied, HAL could work like operator's muscles in the swinging motion, and as a consequence, the muscle activities of the operator were reduced. As a result of this experiment, we confirmed the effectiveness of the proposed method.

Nrf2‐deficient mice are highly susceptible to cigarette smoke‐induced emphysema

Abstract: Inflammation, protease/anti-protease imbalance and oxidative stress play important roles in the pathogenesis of emphysema. Nrf2 counteracts oxidative tissue damage and inflammation through transcriptional activation via the anti-oxidant responsive element (ARE). To clarify the protective role of Nrf2 in the development of emphysema, the susceptibility of Nrf2-knockout mice to cigarette smoke (CS)-induced emphysema was examined. In Nrf2-knockout mice, emphysema was first observed at 8 weeks and exacerbated by 16 weeks following CS-exposure, whereas no pathological abnormalities were observed in wild-type mice. Neutrophilic lung inflammation and permeability lung damage were significantly enhanced in Nrf2-knockout mice 8 weeks after CS-exposure. Importantly, neutrophil elastase activity in bronchoalveolar lavage fluids was markedly higher in Nrf2-knockout mice preceding the pronounced neutrophil accumulation. The expression of secretory leukoprotease inhibitor, a potent inhibitor of neutrophil elastase, was inducible in wild-type, but not in Nrf2-knockout mice. This protease/anti-protease imbalance, together with the lack of inducible expression of ARE-regulated anti-oxidant/anti-inflammatory genes, may explain the predisposition of Nrf2-knockout mice to neutrophilic inflammation. Indeed, specific activators of Nrf2 induced the expression of the SLPI gene in macrophages. These results indicate that Nrf2 protects against the development of emphysema by regulating not only the oxidant/anti-oxidant balance, but also inflammation and the protease/anti-protease balance.